Just my two cents, if you want guild stones to have meaning, they need to be able to do something that you can't do through the guild menu. I'm not sure what that would be.
Perhaps you can only set the guild charter through the guild stone? Maybe you can only declare war through the guild stone? Maybe the only function the guild button should serve would be to recruit, and view the list of members?
Whatever it is, if you want the guild stone to be more than just deco, it needs to do something that you cannot do anywhere else.
As far as the stealing guild stones. Perhaps guild stones should only be able to be placed on the steps of houses that are public. They could then have a sigil on them, like faction sigils, that could be stolen by a guild you are at war with. You cannot log out if you have a guild sigil on you, or enter a house. Stolen sigils can be placed around the base of a guild stone, perhaps two on each face that is showing. If your sigil is stolen all enemy sigils you own are automatically returned to their home guild stones.
Every enemy sigil you have at the base of your guild stone acts like luck for all members of the guild, for all kinds of scrolls, when you are doing champ spawns, or treasure hunts, under either the Fel or Trammel rules set, and improves your chances of getting power scrolls, stat scrolls, sots, scrolls of alacrity, and maybe even forged pardons.
To lessen the chances of abuse you cannot have characters on a single account in more than one guild that is at war. If war is declared by a guild all characters belonging to an account that is already at war are automatically removed from the guild, the war lord receives a warning along with a list of the characters that will be removed if there are any characters that fall under this rule at the time of declaring war.
And now that I think of it, this could be the thing that guild stones do...
